CPH:Triathlon – Race report

Intro

So, my last race report is almost 3 years old by now. I’ve since then raced Egedal Famili
etri
 september 9 2012, and Camilla Pedersen Duathlon October 2013 and lastly Herlev Olympic Tri May 2014.

My daughter was born shortly after Hillerød Tri 2011 which of course naturally shifted priorities. I trained on and off for a year following – 32 km bike commute and swimming and running every now and then. October 2012 a new triathlon club started in Lyngby and I was ready to get some more consistent access to a swimming pool as well as some socializing: All of the above were great races and I had a blast but I were ready for something more again. 2013 came and went but a bout of the flu kept me from Ganløse Tri’s “Tri på Tyren” and nothing more where scheduled.

Preparation

When 2014 was well under way(Late march) and most exisisting races above sprint distance were sold out (For example Øresund Triathlon, Ironman 70.3 Århus etc) and I didn’t have the guts for Full Distance Fyn and other “complete” distance races I was happy to see a new Triathlon, CPH:Triathlon, 1800m swim, 90km bike and 21,1 km run was being prepared in Kastrup I decided to signup thereby getting some distant goal to focus the training around.

The base training was based on:

  • Commute to work (2x 16km) 5 days a week
  • One “long” ride with LSK-Tri sundays
  • 2-3 runs
  • 1-3 swimming sessions with LSK-Tri in the pool

The runs were mostly based on “whatever” I felt like on the day – the swimming around the program made by the poolside coach on the day. Often 2x 1 hour with about 2-2.5k of technique and distance.

As the date drew closer I started looking for some kind of program to get some specific structure into the program towards race day. I settled on an “intermediate” program from tri-radar: “Your Best Ever Ironman 70.3 Training Plan” – a 12week program.

First off I threw away all the swim sets and at first kept on following the pool program of the day and last followed the open water program with LSK-Tri. That was the easiest way for me to actually get any of the sets done.

Then I took a chance and decided to move around the sets within the week to actually fit within my normal weeks and hoping to not compromise too much dedicated recovery etc.

At first I struggled quite a lot adjusting to doing any intensity in the run sets. I felt sluggish and the intensity took it’s toll. Most likely a symptom that I needed it :)

Another “issues” that took some getting used to was that the program only prescribed 2 run work-outs per week. That made it quite a lot easier to actually get it done so that was a huge plus but took some getting used to.

Most of the bike training-sets were based around either x-hours of half-ironman pace or some interval sets. I really enjoyed the interval sets – and couldn’t stand the x-hour TT alone sets. Looking back I should have ditched those workouts and just adapted the group-training-sessions with the club to encompass the same time/intensity goals.

The long bike training sets left me flustered and demotivated, insecure and quite convinced that anything below 2h50 minutes bike-split in the half-ironman distance race would be impossible.

Apart from that the intense(for me) running sets left me quite exhausted but also the fastest I’ve ever been – for me that doesn’t mean much – 5m20s / km for the half-marathon around 1h52 minutes.

Setup

As I the previous years have rented a swimming-wet-suit for the season I this year decided to buy one. I try to use our local shops and triatlonsport.dk (and the owner is an extremly nice guy) had these cool Z3R0D wetsuit and I decided on the “entry”-level Atlante. It seems to fit me quite fine and I love that some color has been incorporated into the design.

On the bike front I had some issues getting a new fork (don’t ask) for my Canyon CF Pro so I ended up buying a completely new bike two weeks before race-day while still waiting for the fork.

I managed a couple of good workouts on the new bike and a bike-fit really hit the spot – the new bike feels awesome!

Raceday

My parents arrived the day before – ready to join my family-cheerleading squad. With regards to food etc. I decided on going with a “i’m 75% LCHF most of the time – leading in to the race i’ll just be MCHF and eat like most people” instead of any “carbo-loading” etc. That being said, to me 5-6 hours of racing doesn’t really warant any extreme measures.

I took a guest bed in our house for the night to not wake up the rest of the family when my alarm went off at 5AM racemorning. Normal breakfast + toast with nutella and a banana and some sis energy drink and coffee to go with that. Then into the car and towards Dragør with a brief stop to pick-up my race-colleague from LSK-Tri, Trine, which had been so kind to pick up my number and stickers saturday.

Running a bit late and driving in MASSIVE rain we were both anxious and exited – with short time to spare – but we made it. A fast entry to T1 to set up the bike and prepare the transition-bag for easy-access.

Swim

(00:36:03)
Then it was a short jog towards the start area as the start time was comming close. As I entered the “arena” (like a outdoor pulic bath house) the first wave of swimmers had just started and my swim wave was in the water getting ready – so I hurried (as seen on the  first image below) to get my gear ready and get into the water. Before we started we saw the peculiar sight that the first swimwave 200m directly out in the water suddenly came out of the water and were walking. But then it was our turn to start to swim. The water was quite restless, waves and rain clouds alround. At the start the mandatory roughing and boxing started but the worst part was that it was almost impossible to see the buoys because of the waves. As we were nearing the first buoy it became obvious to me that we were almost going the wrong way around and had to correct quite alot to pass the buoy to my port-side :). From there we headed “to sea” and at the next buoy we were also forced to walk due to the shallow water. Then a long stretch to the other side with waves and waves and waves (and a bit better space around us).  This was the part were I was thinking “now I’m ready to be done with swimming” – but alas – still more swimming to go. At last we turned the last buoy and we headed towards shore. As we were 200m out from the water-exit the water again turned to shallow and we ran in less than knee high water the last 100-200m. Somewhat illustrated in the second picture below.

 

T1

(00:02:06)
A short run and then time to leave the wetsuite in the transition bag. I decided before hand to put on socks already in T1 so that took some time. On the other hand, for the first time, I tried using tri-shoes with rubber bands attached  to avoid running in bike-shoes. I had practiced it and it worked fine. As expected one of the elastics needed a bit of help to break and then I was off.

Bike

(2:50:29)
As I jumped on the bike I kind of started not entirely centered to use my leg as a buffer from the impact. Turns out that might not have been the best of ideas. 2 minutes later I could feel the same inner thigh acting up and a cramp was starting. The speed was great and on all other fronts I felt great. The rain had stopped and the sun was comming out.

At the first aid station the cramp was more or less setting in full throttle and I was trying all kinds of stuff while telling my self to stay calm, keep breathing etc. Then followed 10k biking with one leg etc. while I tried to get a handle on the cramp. At 20k I finally pulled over and started massaging and stretching while everybody passed my by. Out of all the people passing me by 5-10 women all slowed down and asked me if I was ok. I don’t know if anything can be concluded from that but I really appreciated the sentiment and nodded and said that I was ok.
10 minutes later I could feel that the cramp left and I was left with a sore muscle but workable legs so I took my time getting back up on the bike and started pedaling again.

The bike course was 3 lap course mostly around Amager Fælled with a part along the outer parts of the dike(?) and with the “bird reservation” behind the dike. Very scenic place but potentially windy and not with the widest of roads (bike/foot size road). As it turns out when I got up to speed we arrived at the dike and I checked my average – 20k in 40 minutes. At the time in the “race” I was ecstatic that I was able to overcome the cramps and were very happy that I didn’t have to DNF or other drastic measures.

At the dike I repassed lots of people and unfortunately also 2-3 groups of people drafting in the head wind. I might have said something about it as I passed but all in all it was great to be back at speed and from there on I didn’t really feel the cramps any more.

My fueling strategy for the bike was: 1+L of fluid per hour. Preferably ½L of energy and half a liter of water. On the bike I had two bottle cages for fluids and one for my tools. When i started the bike I had my own energy – 1 with energy-drink, 1 with gels. At each aid-station I would then hopefully be able to exchange a bottle for two bottles – one with water and one with energy – fitting one bottle in my backpocket for a while and one in my aerobar cage. Every hour I would start an energy bar (actually it was mars bars!) and every 20 minutes take a zip of my gel-bottle.

It worked out somewhat OK, but I was kinda forcing the pace a bit to get back up to speed and at the end had trouble getting down more sweet things along with a rumble in the stomach. I still had perhaps one or two gels left in the bottle and was perhaps one bottle of energy behind. It felt ok at the time.

T2

(1m42s)

Off the bike, in to the shoes and straight into an aid-station where Rasmus Henning came trucking along with his 1h116m half-marthon almost done. I jumped out of the way and started drinking coke. The humidity and the temperature was opressing but I tried starting out “on pace”.

Run

(1h54m18s)

As mentioned above the heat was opressing. That’s pretty much it for the run. Overheating, drinking coke and slow running :) I was looking forward to seeing my family and at 4 laps with a narrow loop on it  I could see them sometimes twice on the same loop. That was awesome. As the run moved along and we were running on small suburbia-roads with houses on both sides people were sitting and cheering in their driveways and in the end many brought out the gardenhose so people could be cooled down a bit. Quite the spectacle but it was very nice!
At the finishing lap I was spent – I fought and fought to get back running after walking through the aid-stations, but at least I was passing heaps of people walking lots of  the way.
At the finish-line I passed through and couldn’t see my family – they got lost on the way to portal and arrived a couple of minutes after me :) The nausea came rolling along (and I kinda expected it as I had felt it on my brick sessions in training too) and I just had to sit in the shade, sip water and stare emptily out in the air.

After

As I recovered a bit I was ready to leave the athletes area and went to collect my bike and load up the car. Then it was time to go fetch ice-cream – especially my daughter was looking forward to that. All in all she had been a bit bored but on the other hand had enjoyed being out with her farmor and farfar. After icecream and water it was time to head towards Virum and a great hot day was done.

(Images from Brian HagesenHenrik Hammer, and Jakob Kjeldsen and my wife.)

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New tumblr blog – Confessions of a Copenhagen Bike Commuter

I’ve decided to try out the Tumblr format with a new picture/comment stream at http://confessionsofabikecommuter.tumblr.com/ with a somewhat steady stream of updates (every weekday).

Check it out ;)

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My favorite podcasts

Me and my bike

I bike – alot. Training for triathlon and now also a 2x16km commute every day. Most of that time I listen to podcasts. For the toughest workouts I might switch to music, but most often I really enjoy the podcasts.

I have been listening for podcasts for 4+ years and when I find something I like I get more or less zealous and dread the day when they stop (Im looking at you LugRadio!). I will often change individual ranking, but I am very loyal towards my current list.

With regards to podcast software I used to use my IPod Touch and itunes, but now I’m using my Samsung Galaxy S II and Google Listen

Without further ado (sorted by current internal ranking – best at the top)

  • TechZing -  Jason Roberts and Justin Vincent about being or turning bootstrapped entrepreneur, and their current projects – Pluggio, AppIgnite and AnyFu. I really enjoy both their discussion shows and their excellent interviews. A couple of favorites:

    The best part about TechZing? – They are very productive (twice a week?) and the content level is always high as well as probably the best sound quality of all my podcasts (When using it on the bike, great level mastering is key as well as no-phone-level-quality)

  • This Developer’s Life – By Rob Connery and Scott Hanselman about being a developer – apparently in the format of the highly popular “This American Life”. The sound quality is excellent, the content inspiring, the editing fenomenal and the guests high profile and the angle is quirky and good! Worst thing about it: They dont release very often.
    My favorite past shows:

    • 1.0.3 Problems – about solving problems as a developer – This is the inagural episode that brought Hanselman on board – and illustrated with XKCD, what’s not to like?
    • 1.0.5 Homerun – about those developers that hit a home run. Inspiring
    • 1.1.2 Drive – About drive as a developer, about entrepreneurs. Very inspiring as well
  • Stackoverflow / Stackexchange podcast – By Jeff Atwood and Joel Spolsky (and guests) about the process of building stackoverflow.com and the rest of the stackexchange network. This is a testament to my loyalty. They took a break for almost a year and I never considered unsubscribing from the feed – they might come back :)
    This show is a bit all over the place with regards to topics, so I’m having a hard time selecting specific  favorites

In my next post I will detail the runner ups – or those that gets bumped when one of the above shows up in my queue.

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Hillerød triathlon

Last year I got bitten by the triathlon bug during Copenhagen 4:18:4. Since then I started learning the front-crawl, more biking and consistent running. This spring I even joined KVIK Tri Team here at Amager and that really took my swimming up to a new level.

Come april I bought a road bike: Giant Defy 1. Luckily I at the same time got a coworker bitten by the cycling bug so I had a friend to punish the roads with.

At the same time my wife and I got the news that she is pregnant and we will get a little girl this december. I hear that this entails a complete shift of focus and a change of priorities. This led me to the conclusion: If I want to do a “real” triathlon, this summer is the time in any foreseeable future. I went to the danish triathlon overview page and looked for half ironman races as late in the season as possible: I was seriously considering Silkeborg August 28, but the travel and the clash with Christiansborg Rundt 2k swim race made Hillerød triathlon the obvious choice. 1k swim, 75k bike and 20k run. I had hoped for an openwater swim (and a bit longer) but 50m lanes was a decent compromise. I had hoped for a longer bike as well, but 75k is very decent! 20k run was going to be the hardest part; since last fall my running was lacking due to yet another knee problem.

I signed up, and tried to structurize my training the best as I could after the basic premise: 3 workouts in each diciplin each week.

Today (2011-08-21) was the day of Hillerød tri. Since april 2. I have accumulated 2222km’s on the bike, 430km running, 86km swimming (were the last two months have been open water swimming).

The day started early, 5.10(Am) the alarm went off and I went straight for breakfeast. My usual breakfeast with a banana added and two cups of coffee as well as 750ml of sis energy-drink. I had packed my bags the night before and planned my energy intake: Basic premise: gel every 20minutes from bike start to run end. During the bike I would also take in two energybars (a 30minutes and 1h30minutes – Powerbar Cookies and cream and a Sqeezy Cola Caffeein bar) as well as two times 750ml energy drink.
In the weeks leading up to the race I had been swaying between using the wetsuit or not. (Allthough legal – I feel somewhat cramped around the shoulders and very hot in the pool – but the buoyancy and speed effect is hard to neglect). In the end I packed the wetsuit. I also brought two CO2 cannisters, 3 extra-tubes (only took two on the bike), my new fusion compression top and bottom, cep compresison tubes and extra unattached sleeves for a cold bike ride.

I boarded the  s-train at 6:45 and arrived at the bike-checkin at 7:45ish. Got my number and tried to remember all things I was told at the KVIK tri training seminars about T1/T2 setup and what i’ve learned at 4:18:4.

After that I had to hurry with a shower and change into the wetsuit. Everybody was started with 30seconds intervals in between and my start time was 8:12:00.

At 8:12:01 I jumped into the water and the swimming started. I was number 24 to start so not that many in the pool at that time, and lots of room to overtake and be overtaken in. The layout was to zig-zag the pool for 500meters (in 50m lanes) and then do it once more. Pretty uneventful apart from a single guy that kept tickling me until I stopped at one of the turns to explicitly let him pass. Annoying.

18minutes and 30seconds later(1m51s/100m) I left the pool and ran for T1. In my dreams I had hoped for a 20minute swim but feared a 22 minute swim. Very nice to surpass my own expectations!

The bikecourse was a 2×37,5km loop. As there at most was 20-30people in front of me after the swim not many people to see out on the first loop. Due to road-work they had to direct us through 100m patch of gravel-road. Not fun. And many of the road-side biking-paths were in pretty bad shape. But apart from that it was a beautiful ride (with some wind!). The second loop contained far more people. Both people doing two loops but also the 400persons that was competing in race of half the distance. In the weeks leading into the race I have been struggeling with some pain in my left gluteus maximus(butt cheek) and I was quite annoing today as well. Not debilitating just annoying and taking away my power at that side.

My goal for the bike was to steady my heartrate around 150-155(70-75% HRR) and be

Me in t1 (bit of ISO trouble at the camera)

smart about the nutrition – in best case that would result in a bike-split around 2h20minutes. I had hoped for an aid station with actual bottles instead of just a place to refill my own bottle but what the heck – that minute didn’t hurt me.

When I parked my bike I was happy to see that bike-ride ended at 2h 15m! (33,74 km/t)
Entering T2 I saw my wife with the camera and it always lightens my mood seeing her :)

In T2 I filled my pockets with gels and wielded my running shoes (with elastic shoelaces – fantastic invention). Feeling excellent (I knew that the butt cheek didnt affect my running) I headed for the 2x10km run loops. The route was quite scenic through the woods and along tiny lakes. Lots of people in the woods to run along side. 10k and 5k runners from other racedistances and other 20k runners as well.

The strategy was to settle the heartrate under 160(80%) for the first 10k to ensure that I would survive the last 10k – and no HR caps for the final 10k. Due to my running injuries I havent had a run longer that 10-14k since 2007 – but today was the day! In my last weeks of training 12k was my base run distance so I knew that distance was possible for me to run. So after 8k I told my self: Now you just need to run the 12k you have done so many times during training.

Entering the last part of the run

This summer I entered a 10k race and finished in about 46minutes – based on that I dreamt about a 1h40minute 20k at Hillerød. The first 10k took just about 54 minutes and it felt OK tough my right knee was starting to act up. The second loop was quite tolling and the knee got worse and worse. But somehow I managed to almost keep the pace even finishing with a the last two k a bit faster that the rest. At the finish line I was completely spent. I sat down on the grass an my wife brought me some water. 1h47minutes, and the bike+t2+run was done within 4hours. Inside the exhausted exterior I was ecstatic!

My dream-race was 20minute swim, 2h20m bike, 1h40m run + t1+t2 == 4h26minutes. I finished in all in all 4h21minutes. Way better than I had dared to dream about. Phenomenal!

Now Im sitting in the couch. I ordered both pizza and burger and coke for dinner and my knee is very very sore and I can seem to fight the hunger that keeps on popping up eventhough I eat and eat  – and I feel exhausted, spent, hungover and ecstatic all at once. What a day and worth every hour of training!

After the race - Spent

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KMD 4:18:4 triathlon – 2011

Swim - 4:18:4

Last year I had my debut as triathlete – I wrote about it here: Blogpost last-year

This year I did that same race again. The hardcore numbers:

  • Swim: 7m 15s
  • T1: 03m35s
  • Bike: 28m05s
  • T2: 03m09s
  • Run: 18m12s

All in all  15minutes faster than last year, and still great fun. The major difference is that I have been practicing since last year. Lots and lots of swim, a new bike and a member ship of a triathlon club.

This year they changed bike ride to not include two loops which involved some cobblestones. Otherwise still great fun!

The Swim: This year I had a wet suit! The wind was cold and the water not very warm, so I was very happy to snuggle in my rented nineteen pipeline suit! I have been practicing my crawl technique pretty much since this time last year, so this year it was a breeze to actually do the front crawl all 400m’ers. Except for the part were I got confused and headed for the wrong buoy in the beginning I was plowing through the fields of breast-stroke-swimmers and ran for my bike. (I did not see any backstrokers this year :D)

The Bike: Very uneventful ride. I got a giant defy 1 bike this april and I have mounted aero-bars so it was quite another experience this time around. Nobody to draft from and overtaking all the way! Great fun :)

The run: Hard as all always but I felt stronger and was faster this year, not quite as lonely a run this year either. I believe that triathlon has gotten quite a hold of the danish population!

Great event. My main take-away was to think more about the layout of the transition area. I placed my bike in such a position that I had to run waaaaay to long in my biking shoes (got no triathlon-biking-shoes so I wield the shoes right after the swim and tun out of T1 in them)

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My 2011 races

My tentative raceplan for 2011 (4 triathlons, 2 runs, 1 bike event, 1 swim event):

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Listings definition for the Scala programming language

I’ve tried to find a listings style definition for scala to use in my LaTeX report.

I found a couple of links:

The last (two) link(s) includes a downloadable .sty to include in your LaTeX environment. I had some trouble actually downloading the file so I mirrored it here: http://s3.blog.vrist.dk.s3.amazonaws.com/lstlang0.sty

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Copenhagen 4:18:4 triathlon

Today was the day of Copenhagen 4:18:4 Tri. I had the number 931 sponsored by my employer. The triathlon was roughly a 1/10 of an ironman designed to allow everybody to have a go at a triathlon. I have been flirting with the idea of triathlon ever since I found out how much I like bicycling. My trusty MBK bc7r and me have been around copenhagen for lots of fun as well as the sweaty spinningbikes in Fitnessworld. The last couple of months I have been trying to add some swimming to my weekly training routine. My front-crawl currently only gives me 30-60m before I’m left gasping for air and after 20-30mins of that ok tired, but I might learn it some day.

Today I went ahead and gave it a try anyway. 1000+ contestants was registered and the swim-start was designed to be “start when you want” as in: 50people gets sent of every 3minutes from 17(5pm). Time starts when you run for the water. 4 coworkers and I was signed up and lined up for start around 17.35 and went into the water 17.42. I knew my swim wasnt the good, so I tried to give people space to get into the water in front of me. Nevertheless did I end up in the middel of lots of people and enjoyed the strange feeling of being eaten alive and spit out the back. Very fun, and my crawl (switched to unilateral in 5seconds) was way better than I dared to hope. Direction was hard but fun as well. The swim route was from the beach in the Amager Strandpark Laguna and 200meters out around two bouys and back in.

Leaving the water after 400m

The water was just above 19degree. Neither of my coworkers or I owned a wetsuit so it was just speedo-style.

Somewhere on the swim route a person crossed right in front of me in a leisurely back crawl. What a sight! :)

The water was greenish but it didnt feel too cold. I didnt really have time to ponders such matters at that time anyway.

My swim took 10 minutes and 37seconds. almost 5minutes better than my estimate of 15minutes and it felt ok. My heart was racing and my shoulders could feel that I did actally put some effort into it.

From there I ran straight through the “changing zone”. Nude people werent allowed so if you wanted to change into something else after the swim you had to do it in a tent in the transition zone.

Already yesterday as I was mixing sportsdrink and preparing my bike helmet I decided that my speedos were fine for both biking and running so I ran straight through the chaning zone and on to my bike.

10meters from T2 – From Cph4184

My  bike is a normal city-bike so I had no dedicated bike-shoes and therefore spent the time in T1 tightening my running shoes before I headed out the to the bike course – 5m46s

The bike course was 4.5km down a road with a couple of turns and back again, repeated twice. I have never done any cycling races so this was very exiting for me. Lots of bikes on the road (due to the loop) and no official no-draft rules made for a very fun ride. I rode on as hard as I could while trying to steady my heart – still pounding from the swim. The road was filled with an extremely wide variety of bikes. All the way from granpa-bikes and even a bike with a loading case(christiania bike) and to high-tech disc-wheel time-trial bikes and aero-helmets and everything. Yet another sight.

My legs felt excellent and I love to ride my bicycle so I rode as hard as I dared. During the bike course I caught up to one of my coworkers and took him along on my wheel for a couple of kilometers before he fell behind in a turn. Just after that a “train” of three “real roadbikes” and a tt bike passed me. But not fast enough to frighten me off so I caught up with them. What a feeling: When I got into their slip-stream it felt like the dropped the speed but as soon as I went either side or in a turn the wind hit me hard. I followed along for a couple of kilometers but got cocky and decided to “take my turn” and pass all the way from the back and to the front. 10-30seconds and I was gasping for air again but it felt great and when they soon after overtook me again I was able to hang on to the back again for the last km before T2. The ride took in total 34m33seconds with an average speed of 31.2km/h. Pretty much what I was hoping for.

Leaving T2 going for 4km run

T2 included a pee-break but no change of clothes and took only 3min20sec. Then the run. During the week my right knee area had been bothering me – symptoms somewhat resembling IT-band syndrome which made me back off from any more runs and added lots of streching of the IT-band and icing when possible. Today I felt no problems and the run went fine. I was very glad that I actually had tried to go for a bike-ride and then immediately after go for a run. The feeling of the legs as bricks was recognizable and induced no stress as I was prepared ;) The run was pretty uneventful, but felt somewhat more lonely than the bike-ride. Passed lots of people walking. I run all my runs in a run/walk protocol but had no watch with me. Took a single walk when I felt like it and stretched out my torso a bit to alleviate the side stich that appeared immediately when I started running.

20m12seconds and I passed the finish line. Total time was 1hour 14minutes and 25seconds and I was tired but felt elated and happy.

Drank lots of water and found my coworkers and went for a dip in the water to cool down a bit.

The team – from left: Jan, Mikkel, Daniel, Tue and me

All in all a great event and I was very happy to be able to complete my first triathlon ever! If I had to suggest some improvements I would request some way of getting the overall time somewhere in between as well as a couple of distance markers on the bike and run course.

Apart from that it was fantastic! Thanks to my wife for the support and photo-duty!

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Observations from Amsterdam

Probably trivially obvious and can probably be attributed to my ignorance more than anything around Holland:
  • They really like to drink milk! I denmark we drink milk, but here it is offered for all meals, both at CWI and my hostel
  • For some reason it is easier to get powder milk in your coffee than fresh milk. The mind boggles
  • They like their “fietsen” here. Bicycles almost as many as I see in copenhagen. I’ve seen a fair amount of normal city-bikes with aero-gear. Most of the bikes are “granma-bikes”
  • It is true: Coffee-shops exist and you can walk in and buy hash
  • They are really really really looking forward to the football World Cup in South Africa.
  • They are very proud of their orange colors. Football celebrations and elsewhere
  • Some of the houseboats looks really nice
  • June 9 was electionday for parliment. Very quiet. No posters, no marches, no demonstrations. Very quiet.
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Biomolecular computers and programming

I have recently handed in a report as a part of my masters/candidate in Computer Science at University of CopenhagenVisualizing blobs and computation in a biomolecular computation model“. It sounds very fancy and I would like to introduce the subject and my report here in hopefully a less dry way than in the report it self. (This post will be in a “anecdotal” style and will not contain citations for all the facts. The report above should be up to academic par on citations)

Biomolecular computers and computation

Biomolecular computers or “biocomputers” is an area that have been research the last 20 years. At first much hype and hope was attached that this would provide some kind of break through to overcome the limitations of normal silica-based chip computers as we know and use today – your average PC and every microchip controlled device around. This is the same hope that surrounds quantum computers – a new approach for doing currently very long computations, for example integer factorization of large prime products within feasible time. The jury is still out on the possibility of biomolecular computing to deliver on that hope/potential. Other research have also shown “niche” interest in the area of “DNA Doctor” usage of biocomputers where a “biocomputer” is implemented to interact directly with the cells in for example humans.

A biomolecular computer can be seen as a computer that  “.…use systems of biologically derived molecules, such as DNA and proteins, to perform computational calculations involving storing, retrieving, and processing data.“(From wikipedia). Why is this interesting?

First of all: Why not? Tinkering, and playing around with things is interesting IMHO: By drawing the parallel between a biocomputer and a (human) brain you can say that it is a way to learn about ways nature works.

Second of all, a biocomputer will have different properties compared to conventional computers. Some of the first explored ideas was to use DNA interactions to solve very computational hard problems (NP-complete, traveling salesman like problems, Adleman 1994). This is interesting because it is possible to have millions and millions of molecules in lab-tube and thereby allowing for massively parallel computations – compared to a conventional computer which might have 4 (or at least not millions of) cores for parallel computations.

The Blob programming model

When I contacted my supervisor about writing a project this winter I was introduced to “the blob programming model”. At that time it was mostly an article in progress. Just now it has been accepted for the CS2Bio workshop as “Programming in Biomolecular computation” in Amsterdam, June 10, 2010.

The authors, Neil Jones in particular, read lots of the articles around biomolecular computation, turing universality of the models, and formal algebras for describing molecular interactions (Like Kappa calculus and Biochemical Ground Form) but his background as a computer scientist found something missing: Where are the programs?

Lots of interesting computational properties was proven but as a programmer there is no way to write a program as we know it.

Based on that “hole” a machine language was developed and described in the article which might theoretically could be used on a biocomputer. The models was dubbed “The blob programming model” and the article can be found at http://blobvis.appspot.com/blob

My Project – Visualizations of Blob programs

Based on this article I defined a project for doing a literature review of biocomputing literature as well as visualization theory applicable to visualization of blob programs. Normal progrogramming visualizations exists and have been used for many years, but in this case there was a special angle attached to the visualizations. The blob model has a potential physical analog as it might be possible to create a “biomolecular computer” that can execute the instructions and as the instructions is formed to be somewhat like an abstract molecule or similar a visualization of the blob instruction set could/should reveal interesting properties of blob programs with regards to their physical presence.

A program in the BlobVis tool

At http://blobvis.appspot.com my report is available for download as well as the BlobVis visualization tool I developed. From there you can play around with a few simple “Blob Programs”, for example a “list append'” program and see a video of a program executing in BlobVis. As I focused on physical properties the tool uses a physical based algorithm for layouting the blob programs(Via prefuse) which allows you to drag around programs and data in a way that looks like it is immersed in water or similar. That gives an interesting effect and is fun to watch.

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